Calculate genotype frequencies
Calculate genotype frequencies, by individual or by marker
calc_geno_freq(probs, by = c("individual", "marker"), omit_x = TRUE)probs |
List of arrays of genotype probabilities, as
calculated by |
by |
Whether to summarize by individual or marker |
omit_x |
If TRUE, results are just for the autosomes. If FALSE, results are a list of length two, containing the results for the autosomes and those for the X chromosome. |
If omit_x=TRUE, the result is a matrix of genotype
frequencies; columns are genotypes and rows are either individuals
or markers.
If necessary (that is, if omit_x=FALSE, the data include the
X chromosome, and the set of genotypes on the X chromosome are
different than on the autosomes), the result is a list with two
components (for the autosomes and for the X chromosome), each being
a matrix of genotype frequencies.
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
p <- calc_genoprob(iron, err=0.002)
# genotype frequencies by marker
tab_g <- calc_geno_freq(p, "marker")
# allele frequencies by marker
ap <- genoprob_to_alleleprob(p)
tab_a <- calc_geno_freq(ap, "marker")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.